Kdm3b KDM3B lysine (K)-specific demethylase 3B [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Kdm3bprovided by MGI
Official Full Name: KDM3B lysine (K)-specific demethylase 3Bprovided by MGI
Primary source: MGI:MGI:1923356
See related: Ensembl:ENSMUSG00000038773 AllianceGenome:MGI:1923356
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: JHDM2B; Jmjd1b; mKIAA1082; 5830462I21Rik
Summary: Predicted to enable several functions, including chromatin DNA binding activity; histone H3K9 demethylase activity; and transcription coregulator activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be located in chromatin and nucleoplasm. Predicted to be part of histone deacetylase complex. Is expressed in several structures, including central nervous system; early conceptus; oocyte; and retina nuclear layer. Orthologous to human KDM3B (lysine demethylase 3B). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Ubiquitous expression in CNS E11.5 (RPKM 12.5), thymus adult (RPKM 11.7) and 28 other tissues See more
Orthologs: human all
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Genomic context

Location:: 18 B1; 18 18.73 cM

Exon count:: 24

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	18	NC_000084.7 (34910061..34972423)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	18	NC_000084.6 (34777008..34839370)

Chromosome 18 - NC_000084.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Kdm3b haploinsufficiency impairs the consolidation of cerebellum-dependent motor memory in mice.
Title: Kdm3b haploinsufficiency impairs the consolidation of cerebellum-dependent motor memory in mice.
H3K9 Demethylases JMJD1A and JMJD1B Control Prospermatogonia to Spermatogonia Transition in Mouse Germline.
Title: H3K9 Demethylases JMJD1A and JMJD1B Control Prospermatogonia to Spermatogonia Transition in Mouse Germline.
JMJD1A and JMJD1B, in combination, ensure early embryogenesis and embryonic stem cell viability by establishing the correct Histone 3 lysine 9 methylated epigenome.
Title: Combined Loss of JMJD1A and JMJD1B Reveals Critical Roles for H3K9 Demethylation in the Maintenance of Embryonic Stem Cells and Early Embryogenesis.
findings indicate that Kdm3b is required for normal spermatogenesis and sexual behaviors in male mice
Title: Knockout of the Histone Demethylase Kdm3b Decreases Spermatogenesis and Impairs Male Sexual Behaviors.
These results demonstrate that Kdm3b-mediated H3K9 demethylation plays essential roles in maintenance of the circulating IGF-1, postnatal somatic growth, circulating 17beta-estradiol, and female reproductive function.
Title: The histone H3K9 demethylase Kdm3b is required for somatic growth and female reproductive function.

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Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (5) 1 citation
Gene trapped (2)
Targeted (4) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH124468 (e-PCR)
- UniSTS:161290

RH125340 (e-PCR)
- UniSTS:162162

NoName (e-PCR)
- UniSTS:237773

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables FAD-dependent histone H3K9me/H3K9me2 demethylase activity	IEA Inferred from Electronic Annotation more info
enables antioxidant activity	IEA Inferred from Electronic Annotation more info
enables antioxidant activity	ISO Inferred from Sequence Orthology more info
enables chromatin DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables histone H3K9 demethylase activity	IBA Inferred from Biological aspect of Ancestor more info
enables histone H3K9me/H3K9me2 demethylase activity	IEA Inferred from Electronic Annotation more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables transcription coregulator activity	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
involved_in cellular oxidant detoxification	IEA Inferred from Electronic Annotation more info
involved_in chromatin remodeling	IEA Inferred from Electronic Annotation more info
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
located_in chromatin	IBA Inferred from Biological aspect of Ancestor more info
part_of histone deacetylase complex	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: lysine-specific demethylase 3B

Names: [histone H3]-dimethyl-L-lysine(9) demethylase 3B; jmjC domain-containing histone demethylation protein 2B; jumonji domain containing 1B; jumonji domain-containing protein 1B

NP_001074725.1

EC 1.14.11.65

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001081256.1 → NP_001074725.1 lysine-specific demethylase 3B

See identical proteins and their annotated locations for NP_001074725.1

Status: VALIDATED

Source sequence(s)

AC114820

Consensus CDS

CCDS37761.1

UniProtKB/Swiss-Prot

B9EKS2, Q2VPQ5, Q5U5V7, Q6P9K3, Q6ZPY7, Q8CCE2, Q8K2A5, Q9CU57

Related

ENSMUSP00000037628.8, ENSMUST00000043775.9

Conserved Domains (2) summary

smart00558
Location:1503 → 1575

JmjC; A domain family that is part of the cupin metalloenzyme superfamily

cl40423
Location:1600 → 1705

cupin_RmlC-like; RmlC-like cupin superfamily

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm39 C57BL/6J

Genomic

NC_000084.7 Reference GRCm39 C57BL/6J

Range

34910061..34972423

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_029518.1: Suppressed sequence

Description

NM_029518.1: This RefSeq was suppressed temporarily based on the calculation that the annotated protein was shorter than a protein or proteins from a putative ortholog.